My understanding is that you do earn miles in Aeroflot Bonus if you are ticketed on an SU-designated flight (even if it's operated by a subsidiary/codeshare)
I am not sure if you earn miles in other SkyTeam programs for these same flights though. For instance, Aeroflot Bonus members do not earn miles on DL-designated flights operated by ASA, Comair, etc.
Aeroflot Nord terminated its FFP as of July 1, 2008 and transferred all accounts to Aeroflot Bonus, so you would be earning status with AB.